Abstract:
:Gene expression data have played an essential role in many biomedical studies. When the number of genes is large and sample size is limited, there is a 'lack of information' problem, leading to low-quality findings. To tackle this problem, both horizontal and vertical data integrations have been developed, where vertical integration methods collectively analyze data on gene expressions as well as their regulators (such as mutations, DNA methylation and miRNAs). In this article, we conduct a selective review of vertical data integration methods for gene expression data. The reviewed methods cover both marginal and joint analysis and supervised and unsupervised analysis. The main goal is to provide a sketch of the vertical data integration paradigm without digging into too many technical details. We also briefly discuss potential pitfalls, directions for future developments and application notes.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Wu M,Yi H,Ma Sdoi
10.1093/bib/bbaa169subject
Has Abstractpub_date
2020-08-14 00:00:00eissn
1467-5463issn
1477-4054pii
5892357pub_type
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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doi:10.1093/bib/bbz113
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abstract::While elementary flux mode (EFM) analysis is now recognized as a cornerstone computational technique for cellular pathway analysis and engineering, EFM application to genome-scale models remains computationally prohibitive. This article provides a review of aspects of EFM computation that elucidates bottlenecks in sca...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbt024
更新日期:2013-09-01 00:00:00
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz065
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz040
更新日期:2020-05-21 00:00:00
abstract::The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tool...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/3.1.18
更新日期:2002-03-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbu001
更新日期:2015-03-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbr030
更新日期:2011-09-01 00:00:00
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pub_type: 杂志文章
doi:10.1093/bib/bby104
更新日期:2018-11-07 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa113
更新日期:2020-07-01 00:00:00
abstract::RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a v...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz054
更新日期:2020-07-15 00:00:00
abstract::The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to ident...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
doi:10.1093/bib/bbm048
更新日期:2007-11-01 00:00:00
abstract:BACKGROUND:Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research. METHODS:We assessed the global status of Mtb WGS and developed a 3-week training co...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
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更新日期:2020-10-03 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/1.2.190
更新日期:2000-05-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章,评审
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更新日期:2006-06-01 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbx014
更新日期:2018-09-28 00:00:00
abstract::The Gulbenkian Training Programme in Bioinformatics has been offering hands-on training courses in Oeiras, PT for more than a decade. This article is a review of its functional organization and evolution. We aim to share our experience with people considering setting-up similar training facilities elsewhere. More than...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbq063
更新日期:2010-11-01 00:00:00
abstract::Gene expression profiling holds great potential as a new approach to histological diagnosis and precision medicine of cancers of unknown primary (CUP). Batch effects and different data types greatly decrease the predictive performance of biomarker-based algorithms, and few methods have been widely applied to identify ...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa031
更新日期:2020-04-08 00:00:00
abstract::Synonymous mutations do not change the encoded amino acids but may alter the structure or function of an mRNA in ways that impact gene function. Advances in next generation sequencing technologies have detected numerous synonymous mutations in the human genome. Several computational models have been proposed to predic...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbz047
更新日期:2020-05-21 00:00:00
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journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbv064
更新日期:2016-03-01 00:00:00
abstract::Aberrant DNA methylation is a fundamental characterization of epigenetics for carcinogenesis. Abnormality of DNA methylation-related functional elements (DMFEs) may lead to dysfunction of regulatory genes in the progression of cancers, contributing to prognosis of many cancers. There is an urgent need to construct a t...
journal_title:Briefings in bioinformatics
pub_type: 杂志文章
doi:10.1093/bib/bbaa162
更新日期:2020-08-11 00:00:00
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journal_title:Briefings in bioinformatics
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更新日期:2020-08-25 00:00:00